Potassium in PDB 7qno: Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2

The structure of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2, PDB code: 7qno was solved by G.Kempf, G.Langousis, J.Sanchez, P.Matthias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.34 / 2.38
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	186.134, 186.134, 102.442, 90, 90, 120
R / Rfree (%)	21.2 / 22.8

The structure of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 (pdb code 7qno). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2, PDB code: 7qno:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:K902 b:60.8 occ:1.00 ND1 A:HIS232 2.4 50.3 1.0 OD2 A:ASP323 2.7 42.4 1.0 OD1 A:ASP230 2.8 48.0 1.0 OD2 A:ASP230 2.8 46.2 1.0 O A:HOH1003 2.8 36.3 1.0 OH A:TYR363 2.9 48.5 1.0 HA3 A:GLY361 2.9 60.4 0.0 HB2 A:HIS232 3.0 66.8 0.0 CG A:ASP230 3.1 46.6 1.0 CE1 A:HIS232 3.3 53.0 1.0 HE2 A:TYR363 3.3 59.0 0.0 CG A:HIS232 3.4 50.2 1.0 HE1 A:HIS232 3.4 65.2 0.0 H A:HIS232 3.6 65.6 0.0 CB A:HIS232 3.7 54.4 1.0 CZ A:TYR363 3.8 49.0 1.0 CA A:GLY361 3.9 49.1 1.0 CG A:ASP323 3.9 45.5 1.0 CE2 A:TYR363 3.9 47.9 1.0 NE2 A:HIS192 4.0 47.0 1.0 HG12 A:VAL231 4.0 63.6 0.0 H A:GLY361 4.0 55.1 0.0 HA2 A:GLY361 4.1 60.4 0.0 HE1 A:HIS192 4.2 60.8 0.0 NE2 A:HIS193 4.2 53.6 1.0 N A:GLY361 4.3 44.6 1.0 N A:HIS232 4.3 53.4 1.0 HB3 A:HIS232 4.4 66.8 0.0 NE2 A:HIS232 4.4 52.4 1.0 OD1 A:ASP323 4.5 48.9 1.0 CD2 A:HIS232 4.5 52.8 1.0 CE1 A:HIS192 4.5 49.3 1.0 H A:GLY362 4.5 54.8 0.0 H A:VAL231 4.6 69.8 0.0 CB A:ASP230 4.6 45.7 1.0 CA A:HIS232 4.7 53.0 1.0 C A:GLY361 4.9 44.7 1.0 HB3 A:ASP230 4.9 56.4 0.0 CG1 A:VAL231 5.0 51.8 1.0 HB3 A:GLU360 5.0 59.0 0.0 HB3 A:ASP323 5.0 54.2 0.0

Potassium binding site 2 out of 4 in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:K903 b:72.1 occ:1.00 OG A:SER251 2.7 59.8 1.0 O A:ASP230 2.7 54.1 1.0 O A:HIS232 2.7 52.0 1.0 HB3 A:HIS253 2.7 72.2 0.0 O A:ASP228 2.7 59.7 1.0 OD1 A:ASP228 2.7 57.0 1.0 O A:VAL252 3.0 56.2 1.0 CG A:ASP228 3.2 53.1 1.0 H A:VAL252 3.3 66.1 0.0 HD1 A:HIS253 3.4 71.2 0.0 HA A:HIS233 3.5 71.4 0.0 HB3 A:ASP228 3.5 67.8 0.0 C A:ASP228 3.6 53.3 1.0 C A:VAL252 3.6 56.1 1.0 HA A:SER251 3.6 69.7 0.0 CB A:HIS253 3.6 58.9 1.0 N A:VAL252 3.7 53.8 1.0 C A:HIS232 3.7 53.5 1.0 C A:ASP230 3.7 50.6 1.0 HB3 A:ASP230 3.7 56.4 0.0 CB A:SER251 3.7 55.8 1.0 CB A:ASP228 3.8 55.2 1.0 H A:GLY234 3.9 68.0 0.0 OD2 A:ASP228 3.9 52.5 1.0 H A:ASP230 4.0 60.5 0.0 HB2 A:SER251 4.0 68.5 0.0 N A:ASP230 4.0 49.1 1.0 ND1 A:HIS253 4.0 58.0 1.0 CA A:SER251 4.0 56.8 1.0 C A:SER251 4.1 58.3 1.0 HA A:HIS253 4.2 70.5 0.0 HB2 A:HIS253 4.2 72.2 0.0 HA A:TRP229 4.2 61.1 0.0 CG A:HIS253 4.3 57.0 1.0 CA A:HIS233 4.3 58.2 1.0 CA A:ASP230 4.3 47.1 1.0 CA A:HIS253 4.3 57.5 1.0 CA A:ASP228 4.3 53.1 1.0 N A:HIS253 4.3 56.5 1.0 CA A:VAL252 4.3 56.2 1.0 N A:HIS233 4.4 56.2 1.0 C A:TRP229 4.4 50.0 1.0 HE1 A:HIS192 4.4 60.8 0.0 N A:TRP229 4.4 48.5 1.0 CB A:ASP230 4.4 45.7 1.0 N A:GLY234 4.5 55.4 1.0 HB3 A:SER251 4.5 68.5 0.0 HD1 A:HIS192 4.5 60.1 0.0 CA A:TRP229 4.5 49.6 1.0 N A:HIS232 4.6 53.4 1.0 HG13 A:VAL252 4.6 67.4 0.0 HH A:TYR249 4.6 72.2 0.0 H A:HIS232 4.6 65.6 0.0 HB2 A:ASP228 4.7 67.8 0.0 C A:VAL231 4.7 51.6 1.0 CA A:HIS232 4.8 53.0 1.0 N A:VAL231 4.8 56.9 1.0 HA A:ASP228 4.8 65.3 0.0 C A:HIS233 4.8 56.6 1.0 OH A:TYR249 4.9 58.9 1.0 HA A:VAL231 4.9 62.1 0.0 HG12 A:VAL252 4.9 67.4 0.0 HD2 A:HIS233 4.9 75.6 0.0 HA A:VAL252 4.9 69.0 0.0

Potassium binding site 3 out of 4 in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:K905 b:95.5 occ:1.00 OD2 A:ASP610 2.6 104.8 1.0 CG A:ASP610 2.7 91.4 1.0 O A:HIS614 2.7 106.4 1.0 O A:ASP612 2.7 94.8 1.0 O A:LEU634 2.7 93.7 1.0 O A:ASP610 2.7 97.5 1.0 OD1 A:ASP610 2.8 94.5 1.0 OG A:SER633 2.8 97.0 1.0 HB3 A:HIS635 2.9 115.4 0.0 HA A:HIS615 3.3 114.7 0.0 HB3 A:ASP612 3.4 110.8 0.0 C A:ASP610 3.4 89.0 1.0 H A:LEU634 3.5 119.6 0.0 HB3 A:ASP610 3.5 106.1 0.0 CB A:ASP610 3.6 87.2 1.0 C A:LEU634 3.6 95.0 1.0 C A:ASP612 3.7 94.6 1.0 H A:ASP612 3.7 109.8 0.0 HB2 A:SER633 3.7 113.0 0.0 CB A:SER633 3.7 92.9 1.0 N A:ASP612 3.8 90.2 1.0 C A:HIS614 3.8 100.4 1.0 HA A:SER633 3.8 111.0 0.0 HD1 A:HIS635 3.8 118.1 0.0 CB A:HIS635 3.8 94.9 1.0 N A:LEU634 3.9 98.4 1.0 H A:GLY616 3.9 115.8 0.0 HD2 A:HIS573 4.1 113.6 0.0 CA A:ASP612 4.1 88.3 1.0 HA A:TRP611 4.1 102.1 0.0 CA A:ASP610 4.1 85.3 1.0 CA A:SER633 4.1 91.2 1.0 CB A:ASP612 4.1 91.1 1.0 N A:TRP611 4.2 81.6 1.0 CA A:HIS615 4.2 94.3 1.0 C A:TRP611 4.2 88.0 1.0 HA A:HIS635 4.2 115.5 0.0 HB2 A:HIS635 4.3 115.4 0.0 C A:SER633 4.3 93.9 1.0 CA A:TRP611 4.4 83.8 1.0 N A:HIS615 4.4 97.0 1.0 HH A:TYR631 4.4 109.3 0.0 CA A:HIS635 4.4 94.9 1.0 ND1 A:HIS635 4.4 97.1 1.0 CA A:LEU634 4.4 96.3 1.0 N A:HIS635 4.4 95.8 1.0 HB2 A:ASP610 4.4 106.1 0.0 OH A:TYR631 4.5 89.8 1.0 N A:GLY616 4.5 95.2 1.0 HB3 A:SER633 4.6 113.0 0.0 HA A:ASP610 4.6 103.9 0.0 CG A:HIS635 4.6 93.0 1.0 CD2 A:HIS573 4.7 93.4 1.0 HB2 A:ASP612 4.7 110.8 0.0 N A:HIS614 4.7 100.8 1.0 C A:HIS615 4.8 92.9 1.0 N A:VAL613 4.8 101.4 1.0 C A:VAL613 4.9 99.2 1.0 H A:TRP611 4.9 99.5 0.0 NE2 A:HIS573 4.9 93.6 1.0 H A:HIS614 4.9 122.6 0.0 CA A:HIS614 4.9 102.2 1.0 O A:TRP611 4.9 87.7 1.0 HB2 A:LEU634 5.0 121.6 0.0

Potassium binding site 4 out of 4 in the Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Ligand-Free Danio Rerio HDAC6 CD1 CD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:K906 b:81.4 occ:1.00 O A:PHE241 2.6 76.8 1.0 O A:VAL247 2.7 66.1 1.0 O A:TYR280 2.8 71.0 1.0 O A:ASP244 2.9 81.8 1.0 HB2 A:TYR280 3.0 91.0 0.0 HB3 A:TYR280 3.1 91.0 0.0 HB3 A:PHE241 3.2 82.3 0.0 CB A:TYR280 3.5 74.6 1.0 C A:TYR280 3.5 73.0 1.0 C A:PHE241 3.7 74.7 1.0 H A:ASP244 3.8 100.5 0.0 HB2 A:PHE241 3.8 82.3 0.0 HA A:LEU248 3.8 77.9 0.0 CB A:PHE241 3.9 67.3 1.0 C A:VAL247 3.9 66.3 1.0 HB2 A:ASN281 3.9 87.0 0.0 C A:ASP244 4.0 81.9 1.0 CA A:TYR280 4.1 73.8 1.0 H A:TYR249 4.1 74.5 0.0 HA A:PRO245 4.2 96.6 0.0 HB A:VAL247 4.3 78.8 0.0 HB3 A:ASP244 4.3 92.5 0.0 N A:ASN281 4.3 72.8 1.0 O A:GLY277 4.4 88.2 1.0 H A:VAL247 4.4 88.0 0.0 HA3 A:GLY277 4.4 128.2 0.0 CA A:PHE241 4.4 71.5 1.0 HA A:GLU242 4.4 96.4 0.0 O A:GLU242 4.4 83.6 1.0 HA A:ASN281 4.5 83.3 0.0 N A:ASP244 4.5 82.4 1.0 HA2 A:GLY277 4.6 128.2 0.0 CA A:LEU248 4.6 63.6 1.0 C A:GLU242 4.7 82.3 1.0 N A:LEU248 4.7 67.9 1.0 N A:GLU242 4.7 78.4 1.0 HG12 A:VAL247 4.7 79.4 0.0 HB3 A:TYR249 4.7 71.0 0.0 H A:TYR280 4.7 98.4 0.0 N A:TYR249 4.8 60.8 1.0 CB A:ASN281 4.8 71.2 1.0 CA A:ASP244 4.8 80.9 1.0 CG A:TYR280 4.8 77.6 1.0 CA A:ASN281 4.8 68.2 1.0 HA A:TYR280 4.8 90.2 0.0 HA A:PHE241 4.8 87.4 0.0 CA A:GLU242 4.8 79.0 1.0 CA A:VAL247 4.9 66.2 1.0 N A:PRO245 4.9 79.0 1.0 CA A:GLY277 4.9 105.5 1.0 CA A:PRO245 4.9 79.2 1.0 H A:ASN281 5.0 89.0 0.0 CB A:VAL247 5.0 64.4 1.0 N A:TYR280 5.0 80.8 1.0

G.Langousis, J.Sanchez, G.Kempf, P.Matthias. Expression and Crystallization of HDAC6 Tandem Catalytic Domains. Methods Mol.Biol. V.2589 467 2023.
ISSN: ISSN 1064-3745
PubMed: 36255643
DOI: 10.1007/978-1-0716-2788-4_30